Analysis of Somatic Copy Number Alterations in Biliary Tract Carcinoma Using a Single Nucleotide Polymorphism Array

Figures & data

Table 1. Clinicopathological findings of the biliary tract carcinoma we examined.

	Total (%)	Gallbladder carcinoma (%)	Bile duct carcinoma (%)
Total	36	11 (30.6)	25 (69.4)
Sex
Man	24 (66.7)	5 (20.8)	19 (79.2)
Woman	12 (33.3)	6 (50)	6 (50)
Age (years), median (range)	70 (41–86)	71 (41–84)	70 (45–86)
Location
Gallbladder carcinoma (Gn/Gb/Gf)		2/3/6
Bile duct carcinoma (A/Bi/Bm/Bs/Bp/C)			4/10/5/2/1/3
Size (mm), median (range)	29 (8–123)	45 (15–123)	27 (8–75)
Histological subtype (pap/well/mod/muc/por)	17/10/6/1/2	7/1/1/0/2	10/9/5/1/0
Stage
I	14 (38.9)	3 (21.4)	11 (78.6)
II	17 (47.2)	4 (23.5)	13 (76.5)
III	2 (5.6)	2 (100)	0 (0)
IV	3 (8.3)	2 (66.7)	1 (33.3)
Adjuvant chemotherapy
Done	13 (36.1)	4 (30.8)	9 (69.2)
None	23 (63.9)	7 (30.4)	16 (69.6)
Recurrence
Presence	21 (58.3)	7 (33.3)	14 (66.7)
Absence	15 (41.7)	4 (26.7)	11 (73.3)
Progression-free survival period (days), median (range)	1208.5 (97–4049)	368 (97–4049)	1250 (111–3952)
Mortality
Death	18 (50)	7 (38.9)	11 (61.1)
Survival	18 (50)	4 (22.2)	14 (77.8)
Overall survival period (days), median (range)	1480 (151–4049)	675 (151–4049)	1624 (227–3952)

A: Ampulla of Vater; Bi: Inferior bile duct; Bm: Middle bile duct; Bp: Perihilar bile duct; Bs: Superior bile duct; C: Cystic duct; Gb: Body of gallbladder; Gf: Fundus of gallbladder; Gn: Neck of gallbladder; mod: Moderately differentiated adenocarcinoma; muc: Mucinous carcinoma; pap: Papillary adenocarcinoma; por: Poorly differentiated adenocarcinoma; well: Well differentiated adenocarcinoma.

Figure 1. Hierarchical cluster analysis based on copy number alteration patterns in biliary tract carcinoma.

There were two subgroups that were stratified by cluster analysis in biliary tract carcinoma based on SCNA patterns.

SCNA: Somatic copy number alteration.

Table 2. Clinicopathological findings of each subgroup.

	Total (%)	Subgroup 1 (%)	Subgroup 2 (%)	p-value
Total	36	18 (50)	18 (50)
Sex				0.7247
Man	24 (66.7)	11 (45.8)	13 (54.2)
Woman	12 (33.3)	7 (58.3)	5 (41.7)
Age (years), median (range)	70 (41–86)	70 (41–86)	70 (45–81)	0.6116
Location				0.0027
Gallbladder carcinoma	11	10 (90.9)	1 (9.1)
Bile duct carcinoma	25	8 (32)	17 (68)
Size (mm), median (range)	29 (8–123)	32.5 (15–123)	27.5 (8–75)	0.1966
Histological subtype (pap/well/mod/muc/por)	17/10/6/1/2	9/5/2/0/2	8/5/4/1/0	0.5834
Stage				0.5127
I	14 (38.9)	7 (50)	7 (50)
II	17 (47.2)	7 (41.2)	10 (58.8)
III	2 (5.6)	2 (100)	0 (0)
IV	3 (8.3)	2 (66.7)	1 (33.3)
Adjuvant chemotherapy
Done	13 (36.1)	6 (46.2)	7 (53.8)
None	23 (63.9)	12 (52.2)	11 (47.8)
Recurrence				0.7579
Presence	21 (58.3)	10 (47.6)	11 (52.4)
Absence	15 (41.7)	8 (53.3)	7 (46.7)
Progression-free survival period (days), median (range)	1208.5 (97–4049)	1199 (97–4049)	1208.5 (111–3753)
Mortality				0.5953
Death	18 (50)	9 (50)	9 (50)
Survival	18 (50)	9 (50)	9 (50)
Overall survival period (days), median (range)	1480 (151–4049)	1289 (151–4049)	1643.5 (227–3753)

mod: Moderately differentiated adenocarcinoma; muc: Mucinous carcinoma; pap: Papillary adenocarcinoma; por: Poorly differentiated adenocarcinoma; well: Well differentiated adenocarcinoma.

Figure 2. SCNAs in each subgroup.

(A) Number of loci with somatic copy number alterations in subgroups 1 and 2. There were significant differences in the median numbers of gains and LOHs between subgroups (p < 0.0001). (a) All SCNA patterns; (b) gain pattern; (c) loss of heterozygosity pattern; (d) copy neutral loss of heterozygosity pattern; Number of loci with SCNAs in gall bladder carcinoma and bile duct carcinoma. (e) All SCNA patterns; (f) gain pattern; (g) loss of heterozygosity pattern; (h) copy neutral loss of heterozygosity pattern.

LOH: Loss of heterozygosity; SCNA: Somatic copy number alteration.

Table 3. Significant differences in the frequencies of copy number alterations between subgroup 1 and 2.

Chromosomal regions	Subgroup 1 n = 18 (%)	Subgroup 2 n = 18 (%)	p-value ^†
Gain
7p22.3–p11.1	1–3 (5.6–16.7)	11–15 (61.1–83.3)	<0.01
7q11.21–q22.1	1–2 (5.6–11.1)	10–14 (55.6–77.8)	<0.01
3q26.31–q26.32	2–3 (11.1–16.7)	11–13 (61.1–72.2)	<0.01
20q11.21–q13.33	0–2 (0–11.1)	10–13 (55.6–72.2)	<0.01
3q23–q25.33	1–2 (5.6–11.1)	9–12 (50–66.7)	<0.01
3q27.1, 3q29	2 (11.1)	11 (61.1)	<0.01
2q31.1–q32.3	1–2 (5.6–11.1)	10–11 (55.6–61.1)	<0.01
2q22.1–q24.2	0–1 (0–5.6)	8–11 (44.4–61.1)	<0.01
11q12.2–q14.3	0–1 (0–5.6)	7–11 (38.9–61.1)	<0.01
2q33.2, 2q34 7q31.2–q31.33	1 (5.6)	10 (55.6)	<0.01
1p12, 2q12.1, 2q14.2 2q36.3	1 (5.6)	9 (50)	<0.01
2p23.1–p16.2, 11q24.2–q25	0 (0)	7–9 (38.9–50)	<0.01
2p24.3–p23.3	0 (0)	7–8 (38.9–44.4)	<0.01
8q21.3–q24.22	4–7 (22.2–38.9)	11–15 (61.1–83.3)	<0.05
1q24.1–q24.2	6 (33.3)	13 (72.2)	<0.05
3q26.1–q26.2	3 (16.7)	12 (66.7)	<0.05
17q21.1	4 (22.2)	12 (66.7)	<0.05
17q22	5 (27.8)	12 (66.7)	<0.05
8q11.1–q12.3	4 (22.2)	11–12 (61.1–66.7)	<0.05
1q32.2, 8p11.22, 8p11.1 8q21.11	4 (22.2)	11 (61.1)	<0.05
1q42.11–q44, 3q27.2–q28	3 (16.7)	10–11 (55.6–61.1)	<0.05
2q24.3, 2q33.1, 2q33.3 3q26.33, 7q22.2–q31.1	2 (11.1)	10 (55.6)	<0.05
19q13.31–q13.32, 19q13.41	3 (16.7)	10 (55.6)	<0.05
7q32.1–q34	1–3 (5.6–16.7)	8–10 (44.4–55.6)	<0.05
1p36.23–p36.22, 2q37.1 19q13.43	2 (11.1)	9 (50)	<0.05
2p16.1–p14	1–2 (5.6–11.1)	8–9 (44.4–50)	<0.05
2q12.2–q14.1, 2q35	1 (5.6)	8 (44.4)	<0.05
2p25.3–p25.1	1 (5.6)	7–8 (38.9–44.4)	<0.05
CNLOH
None
LOH
18q22.1–q22.2	7 (38.9)	16 (88.9)	<0.01
19p13.3–p13.2	3–4 (16.7–22.2)	15 (83.3)	<0.01
12q21.1–q24.32	0 (0)	7–12 (38.9–66.7)	<0.01
4q13.1	1 (5.6)	9 (50)	<0.01
17p13.3–p13.2	10–11 (55.6–61.1)	17 (94.4)	<0.05
17p12	11 (61.1)	17 (94.4)	<0.05
9p24.2, 9p21.2	9 (50)	16 (88.9)	<0.05
18q12.2–q21.33	7–8 (38.9–44.4)	15–16 (83.3–88.9)	<0.05
9p13.3–p13.2	6–8 (33.3–44.4)	14–16 (77.8–88.9)	<0.05
14q31.3–q32.33	4 (22.2)	11–12 (61.1–66.7)	<0.05
19p13.13–p13.12	3–4 (16.7–22.2)	11–12 (61.1–66.7)	<0.05
14q23.1, 17p11.1	3 (16.7)	11 (61.1)	<0.05
14q23.3–q24.2, 14q31.1	4 (22.2)	11 (61.1)	<0.05
14q11.2–q12	2–3 (11.1–16.7)	10–11 (55.6–61.1)	<0.05
14q13.2, 14q21.2	3 (16.7)	10 (55.6)	<0.05
12q24.33	1 (5.6)	8 (44.4)	<0.05

† Benjamini–Hochberg false discovery rate adjusted p-value.

CNA: Copy number alteration; CNLOH: Copy-neutral loss of heterozygosity; LOH: Loss of heterozygosity.

Table 4. Significant differences in the frequencies of somatic copy number alterations between gallbladder carcinoma and bile duct carcinoma.

Chromosomal regions	Gallbladder carcinoma n = 11 (%)	Bile duct carcinoma n = 25 (%)	p-value ^†
Gain
7q11.21–q31.33	0 (0)	11–16 (44–64)	<0.05
7p13–p12.2	0 (0)	12–14 (48–56)	<0.05
7p11.1	0 (0)	12 (48)	<0.05
2q31.3	0 (0)	11 (44)	<0.05
CNLOH
None
LOH
None

† Benjamini–Hochberg false discovery rate adjusted p-value.

CNA: Copy number alteration; CNLOH: Copy-neutral loss of heterozygosity; LOH: Loss of heterozygosity.